Publications by authors named "Thomas Litfin"

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Assessing the validity of leucine zipper constructs predicted by AlphaFold.
Isobel Mitic, Keiran Rowell, Thomas Litfin, Katharine A Michie, David A Jacques

Protein Sci· January 2026

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Molecular characterisation of the Bacillus subtilis SpbK antiphage defence system.
Biswa P Mishra, Christian L Loyo, Yanyao Cai, Thomas Litfin, Gause Miraj

Nat Commun· December 2025

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Benchmarking the methods for predicting base pairs in RNA-RNA interactions.
Mei Lang, Thomas Litfin, Ke Chen, Jian Zhan, Yaoqi Zhou

Bioinformatics· June 2025

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Highly Sensitive Spatial Glycomics at Near-Cellular Resolution by On-Slide Derivatization and Mass Spectrometry Imaging.
Cécile Cumin, Lindsay Gee, Thomas Litfin, Ropafadzo Muchabaiwa, Gael Martin

Anal Chem· July 2024

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MARS and RNAcmap3: The Master Database of All Possible RNA Sequences Integrated with RNAcmap for RNA Homology Search.
Ke Chen, Thomas Litfin, Jaswinder Singh, Jian Zhan, Yaoqi Zhou

Genomics Proteomics Bioinformatics· May 2024

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Multiple sequence alignment-based RNA language model and its application to structural inference.
Yikun Zhang, Mei Lang, Jiuhong Jiang, Zhiqiang Gao, Fan Xu, Thomas Litfin

Nucleic Acids Res· January 2024

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3 = 1 + 2: how the divide conquered de novo protein structure prediction and what is next?
Yaoqi Zhou, Thomas Litfin, Jian Zhan

Natl Sci Rev· December 2023

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Predicting RNA distance-based contact maps by integrated deep learning on physics-inferred secondary structure and evolutionary-derived mutational coupling.
Jaswinder Singh, Kuldip Paliwal, Thomas Litfin, Jaspreet Singh, Yaoqi Zhou

Bioinformatics· August 2022

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Probing RNA structures and functions by solvent accessibility: an overview from experimental and computational perspectives.
Md Solayman, Thomas Litfin, Jaswinder Singh, Kuldip Paliwal, Yaoqi Zhou

Brief Bioinform· May 2022

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Reaching alignment-profile-based accuracy in predicting protein secondary and tertiary structural properties without alignment.
Jaspreet Singh, Kuldip Paliwal, Thomas Litfin, Jaswinder Singh, Yaoqi Zhou

Sci Rep· May 2022

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High-throughput split-protein profiling by combining transposon mutagenesis and regulated protein-protein interactions with deep sequencing.
Kai Zhou, Thomas Litfin, Md Solayman, Huijun Zhao, Yaoqi Zhou

Int J Biol Macromol· April 2022

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SPOT-Contact-LM: improving single-sequence-based prediction of protein contact map using a transformer language model.
Jaspreet Singh, Thomas Litfin, Jaswinder Singh, Kuldip Paliwal, Yaoqi Zhou

Bioinformatics· March 2022

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High-throughput mapping of RNA solvent accessibility at the single-nucleotide resolution by RtcB ligation between a fixed 5'-OH-end linker and unique 3'-P-end fragments from hydroxyl radical cleavage.
Md Solayman, Thomas Litfin, Yaoqi Zhou, Jian Zhan

RNA Biol· January 2022

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SPOT-1D-Single: improving the single-sequence-based prediction of protein secondary structure, backbone angles, solvent accessibility and half-sphere exposures using a large training set and ensembled deep learning.
Jaspreet Singh, Thomas Litfin, Kuldip Paliwal, Jaswinder Singh, Anil Kumar Hanumanthappa

Bioinformatics· October 2021

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RNAcmap: a fully automatic pipeline for predicting contact maps of RNAs by evolutionary coupling analysis.
Tongchuan Zhang, Jaswinder Singh, Thomas Litfin, Jian Zhan, Kuldip Paliwal

Bioinformatics· October 2021

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Improved RNA secondary structure and tertiary base-pairing prediction using evolutionary profile, mutational coupling and two-dimensional transfer learning.
Jaswinder Singh, Kuldip Paliwal, Tongchuan Zhang, Jaspreet Singh, Thomas Litfin

Bioinformatics· September 2021

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Systematic Analysis of REBASE Identifies Numerous Type I Restriction-Modification Systems with Duplicated, Distinct Specificity Genes That Can Switch System Specificity by Recombination.
John M Atack, Chengying Guo, Thomas Litfin, Long Yang, Patrick J Blackall

mSystems· July 2020

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Getting to Know Your Neighbor: Protein Structure Prediction Comes of Age with Contextual Machine Learning.
Jack Hanson, Kuldip K Paliwal, Thomas Litfin, Yuedong Yang, Yaoqi Zhou

J Comput Biol· May 2020

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SPOT-Fold: Fragment-Free Protein Structure Prediction Guided by Predicted Backbone Structure and Contact Map.
Yufeng Cai, Xiongjun Li, Zhe Sun, Yutong Lu, Huiying Zhao, Thomas Litfin

J Comput Chem· March 2020

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Identifying molecular recognition features in intrinsically disordered regions of proteins by transfer learning.
Jack Hanson, Thomas Litfin, Kuldip Paliwal, Yaoqi Zhou

Bioinformatics· February 2020

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SPOT-Disorder2: Improved Protein Intrinsic Disorder Prediction by Ensembled Deep Learning.
Jack Hanson, Kuldip K Paliwal, Thomas Litfin, Yaoqi Zhou

Genomics Proteomics Bioinformatics· December 2019

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Nucleotide Sugar Transporter SLC35 Family Structure and Function.
Barbara Hadley, Thomas Litfin, Chris J Day, Thomas Haselhorst, Yaoqi Zhou

Comput Struct Biotechnol J· August 2019

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Improving prediction of protein secondary structure, backbone angles, solvent accessibility and contact numbers by using predicted contact maps and an ensemble of recurrent and residual convolutional neural networks.
Jack Hanson, Kuldip Paliwal, Thomas Litfin, Yuedong Yang, Yaoqi Zhou

Bioinformatics· July 2019

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SPOT-Peptide: Template-Based Prediction of Peptide-Binding Proteins and Peptide-Binding Sites.
Thomas Litfin, Yuedong Yang, Yaoqi Zhou

J Chem Inf Model· February 2019

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Accurate prediction of protein contact maps by coupling residual two-dimensional bidirectional long short-term memory with convolutional neural networks.
Jack Hanson, Kuldip Paliwal, Thomas Litfin, Yuedong Yang, Yaoqi Zhou

Bioinformatics· December 2018

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